Characterization of Apolipoprotein C3 (Apo C3) LNA/DNA Impurities and Degradation Products by LC-MS/MS

Formulas of High MW Unknown Compounds from Accurate Mass Differences and Ranking of Best Candidates from First Principles

The number of possible candidate formulas for high molecular weight unknown compounds (e.g., 7000-8000 Da for common 20-mer oligonucleotides) by high-resolution mass spectrometry is in the order of several hundred thousand even at the highest level of experimental accuracy. In demanding analytical applications involving new chemistries and synthetic routes where little is known about the chemical nature or mechanisms of formation of the unknown compounds (e.g., impurities), the generation of a short list of the most plausible formulas would be highly desirable. Such an approach has been developed in the current work. The concept of mass difference from a reference compound is introduced to simplify the approach and greatly reduce the number of possible formulas. The approach allows for the generation of candidate formulas by both the addition and subtraction of atoms to account for all possible molecular changes from the parent compound. A reduction of 3 orders of magnitude in the number of possible formulas has been achieved by the approach. Ranking of the formulas by the product of the sums of the absolute changes in the total number of all atoms and all heteroatoms in the proposed difference formula successfully ranked the correct formula within the top 10 from a list of 200-250 best candidate formulas. There is a tendency for the impurities to be formed involving the least change in the number of atoms and heteroatoms. ΔfHo and ΔfG'o values can be used as a complementary ranking system of the top candidates. The approach is applicable to unknowns in any other systems of high MW compounds.

Technical Considerations for Use of Oligonucleotide Solution API

The most common approach for the manufacture of oligonucleotides includes isolation of the active pharmaceutical ingredient (API) via lyophilization to provide a solid product, which is then dissolved to provide an aqueous formulation. It is well known from the development and manufacture of large molecules (“biologics”) that API production does not always require isolation of solid API before drug product formulation, and this article provides technical considerations for the analogous use of oligonucleotide API in solution. The primary factor considered is solution stability, and additional factors such as viscosity, concentration, end-to-end manufacturing, microbiological control, packaging, and storage are also discussed. The technical considerations discussed in this article will aid the careful evaluation of the relative advantages and disadvantages of solution versus powder API for a given oligonucleotide drug substance.

Degradation product characterization of therapeutic oligonucleotides using liquid chromatography mass spectrometry

Synthetic antisense phosphorothioate oligonucleotides (PS) have undergone rapid development as novel therapeutic agents. The increasing significance of this class of drugs requires significant investment in the development of quality control methods. The determination of the many degradation pathways of such complex molecules presents a significant challenge. However, an understanding of the potential impurities that may arise is necessary to continue to advance these powerful new therapeutics. In this study, four different antisense oligonucleotides representing several generations of oligonucleotide therapeutic agents were evaluated under various stress conditions (pH, thermal, and oxidative stress) using ion-pairing reversed-phase liquid chromatography tandem mass spectrometry (IP-RPLC-MS/MS) to provide in-depth characterization and identification of the degradation products. The oligonucleotide samples were stressed under different pH values at 45 and 90 °C. The main degradation products were observed to be losses of nucleotide moieties from the 3'- and 5'-terminus, depurination, formation of terminal phosphorothioates, and production of ribose, ribophosphorothioates (Rp), and phosphoribophosphorothioates (pRp). Moreover, the effects of different concentrations of hydrogen peroxide were studied resulting in primarily extensive desulfurization and subsequent oxidation of the phosphorothioate linkage to produce the corresponding phosphodiester. The reaction kinetics for the degradation of the oligonucleotides under the different stress conditions were studied and were found to follow pseudo-first-order kinetics. Differences in rates exist even for oligonucleotides of similar length but consisting of different sequences. Graphical abstract Identification of degradation products across several generations of oligonucleotide therapeutics using LC-MS.